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PubMed1998

Cloning and genomic mapping of the mouse matrin 3 gene and its pseudogenes.

Matrin 3 forms a family of nuclear proteins together with NP220s. Using cDNA sequences encoding rat matrin 3 as a probe, we isolated genomic clones of mouse matrin 3 gene and its two pseudogenes. The genuine mouse matrin 3 gene has an exon covering the N-terminal one third of matrin 3 with a sequence 99% identical to rat matrin 3 cDNA. The gene was localized to Chromosome 18C by in situ hybridization and mapped at 3.6 cM distal to D18Mit117 and 2.2 cM proximal to D18Mit14 on mouse Chromosome 18 by interspecific backcross analysis. One pseudogene has an exon-like sequence covering the N-terminal half of matrin 3 that is interrupted by an unknown sequence. Reverse transcription polymerase chain reaction (RT-PCR) of RNA from mouse liver and brain using unique sequences of the genuine gene and the pseudogene confirmed the expression of only the former. The other pseudogene has a sequence only 80% identical to rat cDNA and is partially deleted and reversed. These pseudogenes were localized to Chromosome 4E2 and 8D2, respectively.

Animals↗
PubMed1997

The rat 5S rRNA bona fide gene repeat maps to chromosome 19q12-->qter and the pseudogene repeat maps to 12q12.

The bona fide 5S rRNA genes in the rat are found in a 1.8-kb tandem repeat and the pseudogenes occur in a 2.5-kb tandem repeat. Three bona fide 5S rRNA genes and one gene variant with one base substitution in the coding region were isolated from the 1.8-kb repeat. Six pseudogenes were isolated from the 2.5-kb repeat. The total number of genes/gene variants/pseudogenes is 700-1200 copies per haploid genome, and the pseudogene repeat contains about 50% more 5S rDNA related sequences compared with the bona fide gene repeat. Various well-defined 5' - and 3'-flanking sequences of the bona fide gene and of the pseudogene were used for in situ hybridization to metaphase chromosomes. The results showed that the bona fide 5S rRNA gene repeat Rn5s maps to chromosome 19q12 and the pseudogene repeat Rn5sp maps to 12q12.

Animals↗
PubMed2004

Packaging and reverse transcription of snRNAs by retroviruses may generate pseudogenes.

Retroviruses specifically package two copies of their RNA genome in each viral particle, along with some small cellular RNAs, including tRNAs and 7S L RNA. We show here that Rous sarcoma virus (RSV) also packages U6 snRNA at approximately one copy per virion. In addition, trace amounts of U1 and U2 snRNAs were detected in purified virus by Northern blotting. U6 snRNA comigrated with the RSV 70S genomic RNA dimer on sucrose gradients. We observed reverse transcription of U6 snRNA in an endogenous reaction in which RSV particles were the source of both reverse transcriptase and RNA substrates. This finding led us to examine mammalian genomic sequences for the presence of snRNA pseudogenes. A survey of the human, mouse, and rat genomes revealed a high number of spliceosomal snRNA pseudogenes. U6 pseudogenes were the most abundant, with approximately 200 copies in each genome. In the human genome, 67% of U6 snRNA pseudogenes, and a significant number of the other snRNA pseudogenes, were associated with LINE, SINE, or retroviral LTR repeat sequences. We propose that the packaging of snRNAs in retroviral particles leads to their reverse transcription in an infected cell and the integration of snRNA/viral recombinants into the host genome.

Animals↗
PubMed2002

SNPs on human chromosomes 21 and 22 -- analysis in terms of protein features and pseudogenes.

SNPs are useful for genome-wide mapping and the study of disease genes. Previous studies have focused on SNPs in specific genes or SNPs pooled from a variety of different sources. Here, a systematic approach to the analysis of SNPs in relation to various features on a genome-wide scale, with emphasis on protein features and pseudogenes, is presented. We have performed a comprehensive analysis of 39,408 SNPs on human chromosomes 21 and 22 from the SNP consortium (TSC) database, where SNPs are obtained by random sequencing using consistent and uniform methods. Our study indicates that the occurrence of SNPs is lowest in exons and higher in repeats, introns and pseudogenes. Moreover, in comparing genes and pseudogenes, we find that the SNP density is higher in pseudogenes and the ratio of nonsynonymous to synonymous changes is also much higher. These observations may be explained by the increased rate of SNP accumulation in pseudogenes, which presumably are not under selective pressure. We have also performed secondary structure prediction on all coding regions and found that there is no preferential distribution of SNPs in a -helices, b -sheets or coils. This could imply that protein structures, in general, can tolerate a wide degree of substitutions. Tables relating to our results are available from http://genecensus.org/pseudogene.

Algorithms↗
PubMed2001

Characterization of a processed pseudogene of human psiHSP40 on chromosome 2q32.

A pseudogene for the human Hsp40 gene has been characterized (psiHSP40). The pseudogene sequence shows 90% similarity to the human Hsp40 mRNA at the nucleotide level. No introns were found in the region corresponding to the human Hsp40 cDNA, and two direct repeats flank this same region. Because of these features, the pseudogene can be classified as a processed pseudogene. PsiHSP40 was assigned to chromosome 2q32 by in situ hybridization. This is the first report of a pseudogene for a member of the DnaJ (Hsp40) family protein gene.

Base Sequence↗
PubMed1991

The snRNP E protein multigene family contains five pseudogenes with common mutations.

Sequence data from three previously-uncharacterized members of the snRNP E protein multigene family suggest that each is a non-transcribed processed pseudogene, even though one clone has the potential to code for a full-length protein with greater than 90% similarity to previously-characterized E protein cDNAs. Each of the newly-analyzed family members is without introns, contains a tract of polyadenylic acid residues, and is flanked by short direct repeats. In addition, the three sequences all contain point mutations that distinguish them from the E protein coding sequence. Seven point mutations are common to the three sequences described here and to two previously-described E protein pseudogenes. Although all of these mutations are transitions, only 5 of 7 could have been generated by deamination of methylated cytosines in inactive genes. Thus, the common mutations in the pseudogenes suggest an origin other than the expressed gene that we have described. Allelic variants for two of the pseudogenes were detected and repetitive elements are located near four of the five E protein pseudogenes that have been characterized.

Amino Acid Sequence↗
PubMed2000

Expression of PTEN and PTEN pseudogene in endometrial carcinoma.

PTEN is a tumor suppressor gene and its mutation is frequently found in endometrial carcinoma. Recently, the pseudogene of PTEN has been reported to be actively transcribed in a number of cells and tissues and a potential for translation is suggested. For further understanding of the involvement of PTEN in endometrial carcinogenesis, we analysed the expressions of PTEN and the pseudogene in 36 endometrial carcinomas with special reference to the genetic status of PTEN. Mutations of PTEN were found in 42% (15/36) of the endometrial carcinomas. The transcript of the pseudogene was expressed in 6 samples (17%) of 36 endometrial carcinomas, but in none of the normal endometria. Western blot analysis showed no translated protein of the pseudogene in any of the cases. Steady level of PTEN protein expression was observed in all the cases examined. Expression level was consistent among the proliferative endometria, secretory endometria and endometrial carcinomas as long as PTEN protein was not truncated. These results indicate that PTEN is a constitutive protein in the endometrium, so that the somatic mutation of PTEN exerts a crucial effect on the endometrial carcinogenesis. In addition, the presence of the PTEN pseudogene transcript urges us caution for the mutational analysis of PTEN as well as careful choice of the probe for the detection of PTEN transcript.

Adult↗
PubMed1988

Embryonic expression of the human 40-kD keratin: evidence from a processed pseudogene sequence.

Analysis of the cytoskeletal components of early murine embryos has detected expression of two keratin proteins, K#8 and K#18, at the 4-8-cell stage. Comparable data for human embryos do not exist, although several processed pseudogenes corresponding to K#8 and K#18 have been discovered in the human genome. Because only genes that are expressed in pre-germ-line and germ-line cells can give rise to processed pseudogenes, the existence of human K#8 and K#18 processed pseudogenes is prima facie evidence for expression of keratins K#8 and K#18 in the early human embryo. We have cloned and determined the complete sequence of a processed pseudogene corresponding to another acidic human keratin. Comparison of its sequence with known sequences of other mammalian keratins indicates that the pseudogene arose from a reverse transcript of a correctly initiated and terminated functional human K#19 gene. This implies expression of K#19 keratin in addition to K#8 and K#18 in the early human embryo. We have proposed previously that K#19 evolved specifically to redress unbalanced production of various basic keratins, and our current evidence, that it is expressed at an early stage of development, implies that K#19 may fulfill this same role during human embryogenesis.

Amino Acid Sequence↗
PubMed1994

[Variability of rDNA genes, detected as a result of analyzing a pseudogene nucleotide sequence in Drosophila melanogaster].

A pseudogene bearing the bulk of the 18S RNA gene was detected outside the rDNA cluster. It comprised irregularly distributed nucleotide substitutions as well as short insertions and deletions. No sequence alterations were observed in the 5' region of the pseudogene, whereas the frequency of substitutions and alterations per nucleotide number in the 3' region and in the middle of the sequence was 7.6% and 1.8%, respectively. The observed sharp irregularity in distribution of substitutions and alterations was considered the result of successive recombinations between the functional 18S rRNA gene and its diverged or damaged variants. This phenomenon provides experimental evidence that recombinations between the pseudogene and functioning repeats of rDNA are implicated in the mechanism of rDNA sequence correction. A segment of the pseudogene sequence was shown to contain substitutions primarily in regions coding for single-strand parts of the RNA molecule. The same segment contained a deletion and an insertion of a nucleotide, approximating it to the most of the studied eukaryotic 18S rRNA sequences. These observations allowed us to supposed that a structural rDNA variant, a fragment of which appears in the pseudogene sequence, is present in the genome. The data obtained suggest both the presence of 18S rDNA variants, and recombination between them, determining the concerted evolution of rRNA genes.

Animals↗
PubMed1997

Sensitive and specific cytokeratin 18 reverse transcription-polymerase chain reaction that excludes amplification of processed pseudogenes from contaminating genomic DNA.

Processed pseudogenes of residual contaminating genomic DNA interfere with a sensitive detection of cytokeratin 18 (CK18) mRNA by reverse transcription and polymerase chain reaction (RT-PCR). This may cause false-positive results when CK18 mRNA is used as a marker for ectopic tumor cells in specimens from cancer patients. To establish a sensitive CK18 RT-PCR by excluding the amplification of processed pseudogenes, the following strategy was chosen: (a) CK18 pseudogene sequences were cloned from genomic DNA by PCR; (b) cDNA-specific primers were designed on the basis of mismatches between pseudogenes and cDNA; (c) PCR conditions were adjusted to reach maximum sensitivity and specificity. Epithelial cells (1-10) could be detected in 1 mL of blood. Among the numerous CK18 genes homologous to the transcribed gene, at least two different processed pseudogenes exist that are highly homologous to each other and to the exons of the transcribed CK18 gene.

Biomarkers, Tumor↗
PubMed1984

Human genes and pseudogenes for the 7SL RNA component of signal recognition particle.

Of the several hundred 7SL RNA-like sequences that are dispersed in human DNA, no more than four are likely to represent genes for 7SL RNA; the majority are 7SL pseudogenes which appear to result from the reverse flow of genetic information from 7SL RNA back into genomic DNA. We present the sequence of five 7SL pseudogenes displaying an unprecedented diversity of structures. All are truncated copies of 7SL RNA, but the site of truncation can occur at either the 5' end, the 3' end or at both ends of the RNA sequence. We suggest that such diverse 7SL pseudogenes are generated by different but related pathways. In particular, we argue that two of the loci are secondary 7SL pseudogenes which derive from RNA polymerase III transcripts of primary (preexisting) 7SL pseudogenes. We also report the isolation and characterisation of a human genomic clone carrying two linked 7SL RNA coding regions, 7L30.1 and 7L30.2. The 7L30.2 locus differs by several single base changes from the known human 7SL RNA sequences and does not appear to be expressed at a detectable level in HeLa cells. The 7L30.1 locus is an authentic 7SL RNA gene encoding one of the three sequence variants of human 7SL RNA.

Base Sequence↗
PubMed1987

Characterization of an HLA-DR beta pseudogene in the DRw52 supertypic group.

The nature of the DR beta II pseudogene in a haplotype of the DRw52 supertypic group was investigated by nucleotide sequence analysis. It revealed several deleterious mutations in the signal sequence and second domain regions in addition to the complete absence of the first domain and adjacent sequences. No expression of DR beta II pseudogene mRNA can be detected. The same DR beta II pseudogene is probably present in other members of the DRw52 supertypic group. The pattern of mutations in this DR beta II pseudogene is different from that observed in the DR beta pseudogene of the DRw53 supertypic group, indicating a distinct evolutionary pathway for these two groups of DR haplotypes.

Amino Acid Sequence↗
PubMed1985

U4 small nuclear RNA pseudogenes from rat genome have common truncated 3'-ends.

Four U4 RNA pseudogenes were isolated and characterized from a rat genomic bank. The four pseudogenes contained sequences completely homologous to U4 RNA from nucleotides 1 to 67 and had common truncated 3'-ends. Three of the four pseudogenes were flanked by 14 to 18 nucleotide-long direct repeats. The structural features of these four U4 RNA pseudogenes are consistent with the hypothesis that these pseudogenes arose by RNA self-primed complementary DNA synthesis and integration into the genome (Van Arsdell et al., Cell 26:11-17, 1981).

Animals↗
PubMed1984

The primate psi beta 1 gene. An ancient beta-globin pseudogene.

The human beta-globin gene cluster contains five functional genes plus a single pseudogene termed psi beta 1. Hybridization and comparative sequence analysis show that this pseudogene is not the product of a recent gene duplication, but is ancient and has been maintained in all major primate groups ranging from prosimians to anthropoids, at the same position as in man, between gamma- and delta-globin genes. In the lemur, a prosimian, the central exons of the psi beta 1 and delta-globin genes have undergone an unequal exchange, which has resulted in a contraction of the beta-globin gene cluster and the formation of a Lepore-type psi beta 1-delta globin pseudogene. Comparisons of defects shared by prosimian, New World monkey and human psi beta 1 sequences suggest that the ancestral primate gene was probably a pseudogene with an abnormal initiation codon but few if any additional defects, and that most contemporary pseudogene defects were accumulated relatively recently by slow neutral drift. We suggest that psi beta 1 arose early in primate evolution by silencing of a pre-existing discrete functional gene, and show that psi beta 1-related sequences are also present in other mammalian orders. In view of the antiquity of psi beta 1-related sequences, we propose that this gene be renamed the eta-globin gene.

Animals↗
PubMed1981

Direct repeats flank three small nuclear RNA pseudogenes in the human genome.

We previously demonstrated that pseudogenes complementary to the small nuclear RNAs U1, U2 and U3 are dispersed and abundant in the human genome. Here we report that three pseudogenes (U1.101, U2.13 and U3.5) are flanked by perfect short direct repeats of 16 to 19 base pairs. In all three pseudogenes. the upstream direct repeat abuts a DNA sequence corresponding to the 5' end of the mature snRNA; in U2.13 and U3.5, the downstream direct repeat immediately follows the truncated 3' end of the snRNA sequence, whereas in U1.101, the downstream direct repeat is separated from the 3, end of the full-length snRNA sequence by a short A-rich region. We consider the direct repeats to be an indication that these three pseudogenes were created by insertion of snRNA information into a new chromosomal locus. To explain why the upstream repeat abuts a DNA sequence complementary to the 5' end of the mature snRNA, we propose a model for insertion that uses a reverse transcript of the snRNA as an intermediate. Furthermore, we note similarities between the structure of all three pseudogene loci and the Alu family of middle repetitive DNA sequences. These similarities suggest that some Alu family sequences are mobile genetic elements that can transpose to new chromosomal loci using as an intermediate a cDNA copy of an RNA transcribed from the Alu family element by RNA polymerase III.

Animals↗
PubMed1981

Two related pseudogenes are the result of a gene duplication in the goat beta-globin locus.

We report the nucleotide sequence of two goat beta-globin pseudogenes, psi beta X and psi beta Z, each of which is linked upstream from a functional goat beta-globin gene. Comparison to the functional beta A gene indicates that these two pseudogenes share several identical mutations. These include alterations of the ATA box, an early frameshift mutation in exon 1 and alterations of the universal GT/AG excision sequence of IVS1. The shared deleterious mutations indicate that the two pseudogenes diverged from a common defective sequence. Comparison of the pseudogenes with the functional beta A and beta C genes reveal that the psi beta X-beta C pair and psi beta Z-beta A pair may have been created by a single en bloc duplication event. The persistence and duplication of defective sequences may indicate a role for these pseudogenes as a spacer or regulator.

Animals↗
PubMed1984

Linkage map of two HLA-SB beta and two HLA-SB alpha-related genes: an intron in one of the SB beta genes contains a processed pseudogene.

Three overlapping cosmid clones contain coding sequences for four HLA Class II genes, provisionally identified as two HLA-SB alpha and two HLA-SB beta genes. The genes are in the order beta, alpha, beta, alpha, inverted with respect to each other. One of the SB beta genes contains a 513 bp sequence that appears to be a processed pseudogene, flanked by direct 17 bp repeat sequences, in the intron upstream of the beta 1 exon. The pseudogene is homologous to a family of sequences of approximately 25-40 members, most of which are not on chromosome 6. A cDNA clone, highly homologous to the pseudogene, except for its 5' end, contains a normal poly(A) addition site and a poly(A) tail. The cDNA clone is homologous to a single-copy gene in both man and mouse, encoded on human chromosome 15. A search of published DNA sequences identified a mouse sequence, with about 77% similarity to the pseudogene sequence, in the negative strand of an intron in a mouse dihydrofolate reductase gene. The second SB beta gene does not contain the pseudogene sequence.

Amino Acid Sequence↗
PubMed2006

Evidence that the gonococcal porA pseudogene is present in a broad range of Neisseria gonorrhoeae strains; suitability as a diagnostic target.

AIMS: The primary aim of the study was to determine if the gonococcal porA pseudogene is a stable sequence target for the detection of Neisseria gonorrhoeae by PCR. METHODS: A total of 240 gonococcal strains from various geographic locations were tested by porA pseudogene PCR. In addition, porA pseudogene PCR positivity rates were compared with established gonococcal assays in three Australian states. RESULTS: All N. gonorrhoeae isolates provided positive results in the porA pseudogene PCR. Positivity rates compared favourably with established gonococcal assays, with increased N. gonorrhoeae detection in the Northern Territory and Western Australia. CONCLUSIONS: The results of this multicentre study provide further evidence that the porA pseudogene is highly conserved across a diverse range N. gonorrhoeae strains and is a suitable PCR target for routine detection of N. gonorrhoeae.

Diagnostic Techniques, Urological↗